Mesh inside soft body - Mesh Deform not working
The problem is with the Mesh Deform modifier. The Mesh Deform only acts on those vertices that are within the Container mesh. In your case you have applied a subdivision surface modifier and this has resulted in some vertices that are outside the container mesh. This means that those vertices are not deformed to follow the softbody simulation and so they are left behind.

To resolve the issue, identify the vertices that are outside and move them within the container and re-bind the Mesh Deform modifier.